[Bioc-devel] bioconductor_docker updates

On Aug 4, 2020, at 6:33 AM, Nitesh Turaga <nturaga.bioc at gmail.com> wrote:

Hi Levi,

Within the RStudio terminal console you can check the contents of the file `/etc/environment`. This should show you a version number 

$ cat /etc/environment
?BIOCONDUCTOR_DOCKER_VERSION = 3.11.11'

(The example above is run on a RELEASE_3_11 image)

Best,

Nitesh 

On Aug 4, 2020, at 4:31 AM, Levi Waldron <lwaldron.research at gmail.com <mailto:lwaldron.research at gmail.com>> wrote:

Thanks Nitesh! Very much appreciated. I was wondering, is there a way to
inspect the version from _within_ the image, i.e., that could supplement a
sessionInfo() command?

On Mon, Aug 3, 2020 at 6:30 PM Turaga, Nitesh <Nitesh.Turaga at roswellpark.org <mailto:Nitesh.Turaga at roswellpark.org>>
wrote:

Hello Bioconductor Community,

A quick update about the latest developments on the Bioconductor Docker
images.

We have updated the ?devel? image to inherit from the latest
?rocker/rstudio:4.0.2? image. This means that the
`bioconductor/Bioconductor_docker:devel` image, which is now available will
be running on,


 1.  Ubuntu 20.04
 2.  R version 4.0.2
 3.  Bioconductor version 3.12.

One major update to the system requirements was the installation of the
?libglpk-dev? which seemed to have caused issues installing the ?igraph?
package. The version number of this image which can be queried through the
docker command is going to be 3.12.13.

If you pull the updates from dockerhub using,

         docker pull bioconductor/Bioconductor_docker:devel

And check the version number using, (the result is going to be 3.12.13.

          docker inspect --format '{{ index .Config.Labels.version}}'
bioconductor/bioconductor_docker:devel


NOTE: The release image stayed exactly the same but with the addition of
the `libglpk-dev` package. The RELEASE_3_11 image did not get updated to
Ubuntu 20.04. It is still based on Ubuntu 18.04. The devel image now works
on a different version of Ubuntu (20.04) as compared to the build system
(18.04. The support for the 18.04 image on rocker is no longer available.

The inspect label command for  RELEASE_3_11 (given below) should produce
the new version number 3.11.11. Do not forget to pull. This is a bug fix
with regards to the igraph package?s missing dependency.

docker inspect --format '{{ index .Config.Labels.version}}'
bioconductor/bioconductor_docker:RELEASE_3_11


If you have any further questions, please reply to this thread.

Best regards,

Nitesh Turaga
Bioconductor Core Team


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-- 

Levi Waldron

Associate Professor

Department of Epidemiology and Biostatistics

CUNY Graduate School of Public Health and Health Policy

Institute for Implementation Science in Population Health

55 W 125th St, New York NY 10035

https://waldronlab.io <https://waldronlab.io/>

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